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- PDB-2jrv: The third dimensional structure of mab198-bound pep.1 for autoimm... -

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Basic information

Entry
Database: PDB / ID: 2jrv
TitleThe third dimensional structure of mab198-bound pep.1 for autoimmune myasthenia gravis
ComponentsPEPTIDE PEP.1
KeywordsIMMUNE SYSTEM / acetylcholine receptor / phage display
MethodSOLUTION NMR / DGSA-distance geometry simulated annealing
AuthorsJung, H.H. / Yi, H.J. / Lee, S.K. / Lee, J.Y. / Jung, H.J. / Yang, S.T. / Eu, Y.-J. / Im, S.-H. / Kim, J.I.
CitationJournal: Biochemistry / Year: 2007
Title: Structural analysis of immunotherapeutic peptides for autoimmune Myasthenia gravis
Authors: Jung, H.H. / Yi, H.J. / Lee, S.K. / Lee, J.Y. / Jung, H.J. / Yang, S.T. / Eu, Y.-J. / Im, S.-H. / Kim, J.I.
History
DepositionJun 29, 2007Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Jul 1, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 9, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_spectrometer ...database_2 / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_spectrometer.model
Revision 1.3May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PEPTIDE PEP.1


Theoretical massNumber of molelcules
Total (without water)1,8831
Polymers1,8831
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 20structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide PEPTIDE PEP.1


Mass: 1883.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Solid Phase Peptide Synthesis

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-1H TOCSY
1212D 1H-1H COSY
1312D 1H-1H NOESY

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Sample preparation

DetailsContents: 1mM protein; 90% H2O, 10% D2O / Solvent system: 90% H2O/10% D2O
SampleConc.: 1 mM / Component: protein
Sample conditionspH: 6.1 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
X-PLORBrungerrefinement
X-PLORBrungerchemical shift assignment
ANSIG3.3Kraulischemical shift assignment
RefinementMethod: DGSA-distance geometry simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 20 / Conformers submitted total number: 20 / Maximum lower distance constraint violation: 1.8 Å / Maximum upper distance constraint violation: 6 Å / Torsion angle constraint violation method: PROCHECK_NMR
NMR ensemble rmsDistance rms dev: 0.93 Å / Distance rms dev error: 0.32 Å

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